LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix ehex to add/subtract energy from 2 regions

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 20

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
lattice		fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region		box block 0 $x 0 $y 0 $z
region		box block 0 10 0 $y 0 $z
region		box block 0 10 0 10 0 $z
region		box block 0 10 0 10 0 20
create_box	1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
  2 by 1 by 4 MPI processor grid
create_atoms	1 box
Created 8000 atoms
mass		1 1.0

velocity	all create $t 87287
velocity	all create 1.35 87287

pair_style	lj/cut ${rc}
pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 10 11
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp $t $t 0.5
fix             1 all nvt temp 1.35 $t 0.5
fix             1 all nvt temp 1.35 1.35 0.5
thermo	        100
run             1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms

Performance: 485876.777 tau/day, 1124.715 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48042    | 0.50311    | 0.52772    |   1.9 | 56.59
Neigh   | 0.22997    | 0.23203    | 0.23466    |   0.3 | 26.10
Comm    | 0.081187   | 0.10484    | 0.1285     |   4.2 | 11.79
Output  | 0.00027299 | 0.00028226 | 0.000314   |   0.1 |  0.03
Modify  | 0.028298   | 0.032276   | 0.037612   |   2.0 |  3.63
Other   |            | 0.01658    |            |       |  1.86

Nlocal:    1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost:    2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs:    27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1

Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0

velocity	all scale $t
velocity	all scale 1.35

unfix		1

# 2nd equilibration run

fix		1 all nve
fix             hot all ehex 1 100.0 region hot
fix             cold all ehex 1 -100.0 region cold

thermo_style    custom step temp c_Thot c_Tcold
thermo	        1000
run             10000
Memory usage per processor = 2.80761 Mbytes
Step Temp c_Thot c_Tcold 
    1000         1.35     1.431295    1.2955644 
    2000    1.3537291    1.6418772    1.1875127 
    3000    1.3615152    1.6451299    1.1769094 
    4000    1.3612129    1.5281727    1.2022419 
    5000    1.3552182    1.6672955    1.2212864 
    6000    1.3643442    1.6072213    1.2390567 
    7000    1.3665773    1.6909819    1.1466611 
    8000     1.375741    1.6144274    1.1691231 
    9000    1.3701136    1.8238424     1.136342 
   10000    1.3563004    1.8059065    1.1547129 
   11000    1.3794051     1.692299    1.0515688 
Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms

Performance: 409265.976 tau/day, 947.375 timesteps/s
99.4% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.1863     | 5.0134     | 5.8326     |  28.0 | 47.50
Neigh   | 2.1559     | 2.4232     | 2.6516     |  14.2 | 22.96
Comm    | 0.80561    | 1.8126     | 2.8852     |  58.4 | 17.17
Output  | 0.00044537 | 0.00064856 | 0.00077057 |   0.5 |  0.01
Modify  | 0.81915    | 0.94285    | 1.0571     |   9.5 |  8.93
Other   |            | 0.3628     |            |       |  3.44

Nlocal:    1000 ave 1105 max 883 min
Histogram: 1 1 2 0 0 0 0 0 2 2
Nghost:    2319.38 ave 2502 max 2114 min
Histogram: 1 3 0 0 0 0 0 0 0 4
Neighs:    27387.9 ave 32453 max 21803 min
Histogram: 2 2 0 0 0 0 0 0 0 4

Total # of neighbors = 219103
Ave neighs/atom = 27.3879
Neighbor list builds = 1696
Dangerous builds = 0

# thermal conductivity calculation

compute		ke all ke/atom
variable	temp atom c_ke/1.5

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex

variable        tdiff equal f_2[11][3]-f_2[1][3]
fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave

run             20000
Memory usage per processor = 3.0578 Mbytes
Step Temp c_Thot c_Tcold v_tdiff f_ave 
   11000    1.3794051    1.6903393    1.0515688            0            0 
   12000    1.3799777    1.8004888    1.1032219  -0.63860014            0 
   13000    1.3733605    1.7823094    1.0553582  -0.65827891  -0.65827891 
   14000    1.3749743    1.7852256    1.1674016  -0.68463005  -0.67145448 
   15000    1.3863795    1.8538127    1.0056247  -0.73524813  -0.69271903 
   16000    1.3731955    1.7518546    1.0741458  -0.74810775  -0.70656621 
   17000    1.3771856    1.9016869    1.0090502  -0.73999567   -0.7132521 
   18000    1.3766032    1.7616195    1.1142155  -0.73769104  -0.71732526 
   19000    1.3815934    1.7791247    1.1406987  -0.73617832  -0.72001855 
   20000    1.3725543    1.8637436    1.0799364  -0.73435569   -0.7218107 
   21000    1.3817369    1.8808771    1.0642524  -0.76702329  -0.72683432 
   22000    1.3968704     1.840287     1.072304  -0.82496419   -0.7366473 
   23000    1.3895558    1.9427293    1.0766665  -0.75363908  -0.73819201 
   24000    1.3900493    1.9883976    1.1081017  -0.86394774  -0.74867166 
   25000    1.3838912    1.8853041    1.0795751  -0.83043902  -0.75496145 
   26000    1.3912105    1.9330259    1.1070335  -0.79880182  -0.75809291 
   27000    1.3891151    1.8548451    1.0676153  -0.81856523   -0.7621244 
   28000    1.3942624    1.9796706    1.1251407  -0.81762456  -0.76559316 
   29000    1.3819302    1.8619138    1.0495292  -0.78627491  -0.76680973 
   30000    1.3968366     1.883107    1.1004588  -0.83902548  -0.77082172 
   31000    1.3822489    1.8220413    1.0322271   -0.7550338  -0.76999077 
Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms

Performance: 379649.018 tau/day, 878.817 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.4811     | 10.102     | 12.63      |  68.7 | 44.39
Neigh   | 4.0495     | 4.9884     | 5.8366     |  37.8 | 21.92
Comm    | 1.6695     | 4.9483     | 8.493      | 130.7 | 21.74
Output  | 0.0010517  | 0.0017769  | 0.0019059  |   0.7 |  0.01
Modify  | 1.6903     | 1.9371     | 2.2355     |  14.8 |  8.51
Other   |            | 0.7799     |            |       |  3.43

Nlocal:    1000 ave 1121 max 857 min
Histogram: 2 0 1 1 0 0 0 0 1 3
Nghost:    2299.75 ave 2541 max 2067 min
Histogram: 3 1 0 0 0 0 0 0 2 2
Neighs:    27487.2 ave 33361 max 20651 min
Histogram: 2 1 1 0 0 0 0 0 0 4

Total # of neighbors = 219898
Ave neighs/atom = 27.4872
Neighbor list builds = 3474
Dangerous builds = 0
Total wall time: 0:00:34
